MolNFT v1 · #51335 · protein
A non-cytotoxic dsred variant for whole-cell labeling
2V4E · Red fluorescent protein DRFP583: “A non-cytotoxic dsred variant for whole-cell labeling”. X-ray diffraction, 1 ligand (NRQ), 20 pockets (best druggability 0.84). MolNFT v1 #51335 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2V4E
- Type
- protein
- Length
- 1,734 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Red fluorescent protein DRFP583
- Ligands
- NRQ
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Red fluorescent protein DRFP583 | protein | 216 | 5% helix, 57% strand | — |
| B | Red fluorescent protein DRFP583 | protein | 217 | 5% helix, 57% strand | — |
| C, D, F, G, H | Red fluorescent protein DRFP583 | protein | 217 | 5% helix, 57% strand | — |
| E | Red fluorescent protein DRFP583 | protein | 216 | 3% helix, 57% strand | — |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.84 | 0.85 | 96 | empty |
| 2 | 1040 | 0.83 | 0.85 | 96 | empty |
| 3 | 95 | 0.77 | 0.98 | 31 | NRQ |
| 4 | 93 | 0.76 | 0.97 | 29 | NRQ |
| 5 | 92 | 0.75 | 0.97 | 30 | NRQ |
Interfaces
11 interfaces between chains.
- A–B · 1404 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1400 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1396 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1387 Ų buried · 17 hydrogen bonds · protein-protein
- F–H · 1086 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (chromophore).
Compared structures
- 2V4E · A non-cytotoxic DsRed variant for whole-cell labeling · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2V4E · PDBe 2V4E
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